Guidance

Pathogen genomics at Porton Down user manual

Published 26 March 2024

Introduction

The Pathogen Genomics Department at Porton Down provides a sequencing service for SARS-CoV-2 for customers across the NHS and UKHSA. The laboratory at Porton Down sequences the samples and the UKHSA Bioinformatics department performs analysis of the data to determine a SARS-CoV-2 variant result. Sequencing is essential for identifying and managing the emergence of variants of concern. The results will also be sent via the Second-Generation Surveillance System (SGSS) and through to government for key decision making around Variants of Concern.

This document provides details on how to send samples for sequencing at UKHSA Porton Down. The service is being offered for public health surveillance purposes and not as a diagnostic service. Trusts will not be charged for referring Pillar 1 NHS samples, that have been identified as SARS-CoV-2 PCR positive, to UKHSA Porton Down for whole genome sequencing.

Please note if sending different types of samples to Porton Down for testing by different departments these must be packaged separately. All Covid samples for genome sequencing should be packaged on their own. This allows the correct samples to be directed to the relevant department and ensure these are handled in a safe manner within the correct facilities.

Disclaimer

This document has been controlled under the UKHSA Document Control System. Any printed copy becomes an uncontrolled document and is not managed under the UKHSA Document Control System. It is the responsibility of the copy holder to ensure that any hard copy or locally held copy in their possession reflects the current version available from the UKHSA internet site.

Amendment history

From 1 January 2024, this document fully replaces the preceding user manual (named GENW004 version 1).

Establishment of service agreement

Each request accepted by the laboratory for examination is considered to be an agreement under UKHSA terms and conditions of business. Specific requests for service level agreements or contracts should be made to business@ukhsa.gov.uk.

Key personnel and contact details

Head of Operations, Genomics Service Delivery and Quality

Catherine Ryan
Email: catherine.ryan@ukhsa.gov.uk
Telephone: 0208 327 7549

National Quality Lead for Genomics

Ebere Otuka
Email: ebere.otuka@ukhsa.gov.uk
Telephone: 0282 133 4551

Technical Manager, Pathogen Genomics, Porton Down

Rai Broadway
Email: karlyrai.broadway@ukhsa.gov.uk
Telephone: 02078117394

Services available

Pathogen Genomics Porton Down Laboratory offers whole genome sequencing testing of SARS-CoV-2 samples.

Turnaround times (TAT) are from day of sample receipt to the day of report issue in Calendar days.

The department aims for a maximum 7 day turnaround time on results. If the lab is operating a longer lead time or experiencing major delays that may impact on patient care, this will be communicated to users.

Please take note of the instructions regarding sample specifications and information to be provided, as any missing or inaccurate information can cause delays in sample processing.

How to obtain services

Hours of service

UKHSA Porton Down are open to receive samples 7 days per week, however there is no requirement to send samples on Saturdays and Sundays. Samples should be sent on the next working day. If the sample has to be stored until the next working day, samples must be refrigerated until they are sent.

Normal laboratory opening times are between 9am and 5pm, Monday to Friday (excluding bank holidays).

Services to the public

Pathogen Genomics Porton Down Laboratory does not offer diagnostic services to members of the public. Results can only be issued to the requesting physician or medical unit and will not be given to patients directly under any circumstance. We reserve the right to check the authenticity of callers in order to protect the confidentiality of patients’ personal data.

There are no clinical facilities at UKHSA Porton Down and we are unable to see patients or give telephone medical advice directly to members of the public.

Laboratory location

The Pathogen Genomics department is situated in the Henderson Wing at UKHSA Porton Down. The address is:

UKHSA Porton Down Manor Farm Road
Porton Down, Near Salisbury Wiltshire
SP4 0JG

Specimen submission guidelines

All samples must be labelled with the following information:

• surname, forename or other unique patient identifier
• date of birth
• NHS number
• senders reference/sample number
• date of sample collection.

It is also useful for the laboratory to know the cycle threshold (Ct) from the SARS-CoV-2 PCR test so please include this information if available.

Only samples with Ct values <30 in at least one of the multiple targets should be referred for sequencing testing. Positive samples detected using methods without Ct (qualitative tests) can be submitted but may fail to produce a reportable result in sequencing assays where the viral load is very low.

If using a platform which does not provide a Ct value, for example, if it uses RLU or Cn values, please send all specimens which are reported as positive, and the equivalent value should be included on the sample request form if this information is available.

Request forms

Samples must be sent with either the NPEx manifest or the P6 COVID-19 Genome Sequencing - Porton Request Form.

It is important that the NPEx manifest or P6 request form is completed as fully as possible and must include sample collection date.

Place the NPEx manifest or copy of the form in the parcel (not in contact with the specimen container) indicating relevant safety information and sample types.

Request on NPEx when possible as this is the laboratory’s preferred requesting method. Only complete the P6 request form where electronic requesting is not available. The laboratory can be contacted to set up electronic requesting via NPEx.

Specimen quarantine

Failure to complete relevant information on the request form may lead to the specimen being placed in quarantine on arrival at the laboratory, and subsequent delays in processing whilst further information is sought from the referring laboratory. Please ensure all relevant clinical information is completed on the forms.

In the event of a specimen being quarantined, the referring laboratory will be contacted to provide further information. Where no response is received and hence no testing is performed, the samples will be kept for a minimum of one month, after which they may be discarded.

Specimen transportation

Please preferentially use DX to transport samples to UKHSA Porton Down. UKHSA does not provide DX boxes, laboratories will need to secure these through their usual procurement system. Samples are to be transported at ambient temperature.

The Porton Down DX address:

DX 6930407 SALISBURY 92 SP
P30, Molecular Henderson Wing UKHSA Porton Down
Manor Farm Road
Porton Down, Near Salisbury Wiltshire
SP4 0JG

If transportation using DX is not possible, samples can be sent via courier, using details below:

• City Sprint: Telephone 0117 304 1374
• quote account reference: CS013545, password PHEDAB
• please specify the service does not need dry ice

Samples should not be sent via courier on a Saturday or Sunday. Samples should be sent on the next working day.

Materials containing live virus need to be managed as ACDP Hazard Group 3 specimens and must comply with UN3373 P650 packaging and labelling.

For details on how to package samples please see the packaging and transport requirements for patient samples - UN3373

Please place a UN3373 label on the outer packaging with postal address and annotation of P30, to ensure the samples are directed to the correct laboratory.

Please note if sending different types of samples to Porton Down for testing by different departments these must be packaged separately. All Covid samples for genome sequencing should be packaged on their own. This allows the correct samples to be directed to the relevant department and ensure these are handled in a safe manner within the correct facilities.

Sample types for SARS-CoV-2 Sequencing

Nose and/or throat swabs in viral transport medium (VTM) are the preferred specimens for SARS-CoV-2 Sequencing. Other specimens such as sputum of bronchoalveolar lavage (BAL) are not suitable. Standard swabs and containers must be used.

A minimum primary sample volume of 400µl is required, though its preferable to receive >600µl. If there is no access to original sample, re-swabbing is recommended. Do not batch samples together, please send samples as soon as available as described in section 7.1.

Sample rejection criteria

Samples will be rejected if:

• their volume is less than that specified for the service
• the Ct value listed is outside of the specified cut-off
• a request form (or suitable alternative) has not been completed
• they are Incorrectly labelled; missing information such as surname, forename, date of birth or NHS number
• they do not reference a sender’s reference/sample number
• do not reference a date of sample collection

Key factors affecting tests

Some sample collection buffers are not suitable for the sequencing pathway. This is because the chemical lysis buffer is detrimental to the integrity of RNA. Failed sequencing runs offer poor public health value for money and delays public health responses. Specific instructions for unsuitable lysis buffers are detailed below.

The following sample buffers are not suitable:

• Samba/Liat buffer. Instead, please send original sample in VTM or re-swab within 48 hours

Please clearly indicate the lysis buffer used on the sample request form. Failure to provide this safety critical information may delay processing of the sample and could affect the quality of sequencing result.

To ensure a successful sequencing result, it is also important that the laboratory receives a minimum sample volume of 400µl, and samples have generated a positive PCR result with Ct values <30.

Tests available

Pathogen Genomics Porton Down Laboratory offers whole genome sequencing testing of SARS-CoV-2 samples.

Reports

Results will be issued back to the requesting organisations via the original request route (for example via NPEx). For organisations that do not have electronic reporting route, results will be reported back via eLab.

For details on how to register for E-lab and any general queries, please contact: eLAB.Helpdesk@ukhsa.gov.uk. This operates Monday – Friday, 9am – 5pm.

Policy on emailing reports

The following guidelines have been prepared having taken into account the code of practice on reporting patients’ results by email prepared by the Department of Health and Caldicott recommendations.

• it is UKHSA policy that reports containing patients’ data should not be sent by email
• emails cannot be relied on to guarantee security of patients’ data because they can be intercepted by a third party
• reports cannot be sent by fax

  Additional information on SARS-CoV-2 sequencing results

You can view the Standardised Variant Definitions. This is a repository containing the up-to-date lineage definitions for variants of concern (VOC) and variants under investigation (VUI) as curated by UKHSA.

If a sample is unable to be tested for any reason the sample will be marked as rejected and the user notified.

Quality assurance in pathogen genomics

Accreditation

Pathogen Genomics Porton Down Laboratory is currently unaccredited however is working towards ISO15189:2022 accreditation for its SARS-CoV-2 sequencing test.

External quality assurance

Pathogen Genomics Porton Down Laboratory participates in these where available and appropriate for the examination. Any issues with EQA performance which could affect any of the services provided are communicated directly to users where relevant. Results of EQA performance are discussed at Management Review meetings.

Service updates

Users will be informed of any delays beyond the published turnaround times where these could compromise or have an impact on patient care.

Authorisation of reports

Staff authorising reports are competency assessed and are state registered HCPC Biomedical Scientists. Issue of revised reports: any amendments to original reports will be highlighted to users.

Key contact for general quality-related enquiries:

Quality Assurance Manager, Pathogen Genomics Porton Down Laboratory

Becca Bennett
Email: becca.bennett@ukhsa.gov.uk Telephone: 020 7123 3681

Enquiries and complaints

If you would like to report a problem, or you are not satisfied with the service you have received please contact the Complaints Manager using the details below.

Complaints will be responded to within 20 days of notification. Resolution of complaints will be undertaken within the shortest timeframe achievable. If resolution cannot be achieved within 20 days, the complainant will be notified.

Our endeavour is to be responsive to the changing needs of all users of our services. We welcome comments and feedback on the provision of our services.

Contact: Rai Broadway, Technical Manager
Email: karlyrai.broadway@ukhsa.gov.uk Telephone: 020 7811 7394

For any enquiries relating to SARS-CoV-2 sequencing or the UKHSA Pathogen Genomics Service, these should be sent to the laboratory directly. The contact details above should also be used.

Recognition of Caldicott recommendations

The recommendations of the Caldicott Report (1997) and the subsequent Information Governance Review (2013) have been adopted by UKHSA and by the NHS as a whole. These recommendations relate to the security of patient identifying data (PID) and the uses to which they are put. UKHSA observes Caldicott guidance in handling PID and has appointed its own Caldicott Guardian. They advise others on confidentiality issues and is responsible for monitoring the physical security of PID in all parts of the Porton Down site. This also applies to the transfer of results of investigations to and from the site whether by mail services or telephone.

UKHSA is keen to audit the security of its PID in collaboration with its customers. Customers are invited to review our arrangements in conjunction with individual laboratory directors and/or the Caldicott Guardian. Customers are also asked to draw to the Caldicott Guardian’s attention any instances where PID security has been threatened or has broken down. Uses that PID are put to outside clinical diagnostic services generally allow patient identifiers to have been removed beforehand, and when PID is used for research purposes the proposals are considered first by the UKHSA Research Ethics Committee. All enquiries about the security and use of PID at UKHSA should be addressed to the UKHSA Caldicott Guardian at: caldicott@ukhsa.gov.uk

UKHSA is compliant with both the UK General Data Protection Regulation (GDPR) and Data Protection Act 2018.

Sample retention and disposal

Results and patient information are stored and maintained according to the Royal College of Pathologists “The retention and storage of pathological records and specimens schedule” and also in accordance with DHSC records management policy and local record retention policy. Results are reported back to the sender as detailed in Section 11 of this document.

UKHSA complies with the Human Tissue Act with clear guidance on the use, storage and disposal of human tissues received by UKHSA laboratories. The specification for samples received for SARS-CoV-2 sequencing does not include human tissues, but the system established for this sample type ensures samples are to be treated with due care and respect.